Inland waters emit and export large quantities of carbon (C), and the balance between emission and export determines the role of inland waters in the global C cycle. Modeling studies of stream-lake networks suggest that C emission-to-export ratios (emission:export) are higher in lake-rich networks with longer network residence times (NRT), yet empirical evidence supporting these patterns remains limited. We sampled 362 stream segments and 42 lakes across 32 nested arctic stream-lake networks, repeated across four seasons with contrasting environmental conditions. The data show that lake-rich networks have much longer NRT and higher C emission:export regardless of environmental conditions, while overall C emission:export increased during warmer low-flow periods. Our findings stress the importance of accounting for lakes within stream networks and simultaneously quantifying multiple C fates when assessing the role of inland waters in the C cycle.